The present invention relates to molecular biology and pharmacology. More particularly, the invention relates to calcium channel compositions and methods of making and using the same.
Calcium channels are membrane-spanning, multi-subunit proteins that allow controlled entry of Ca2+ ions into cells from the extracellular fluid. Cells throughout the animal kingdom, and at least some bacterial, fungal and plant cells, possess one or more types of calcium channel.
The most common type of calcium channel is voltage dependent. All xe2x80x9cexcitablexe2x80x9d cells in animals, such as neurons of the central nervous system (CNS), peripheral nerve cells and muscle cells, including those of skeletal muscles, cardiac muscles, and venous and arterial smooth muscles, have voltage-dependent calcium channels. xe2x80x9cOpeningxe2x80x9d of a voltage-dependent channel to allow an influx of Ca2+ ions into the cells requires a depolarization to a certain level of the potential difference between the inside of the cell bearing the channel and the extracellular environment bathing the cell. The rate of influx of Ca2+ into the cell depends on this potential difference.
Multiple types of calcium channels have been identified in mammalian cells from various tissues, including skeletal muscle, cardiac muscle, lung, smooth muscle and brain, [see, e.g., Bean, B. P. (1989) Ann. Rev. Physiol. 51:367-384 and Hess, P. (1990) Ann. Rev. Neurosci. 56:337]. The different types of calcium channels have been broadly categorized into four classes, L-, T-, N-, and P-type, distinguished by current kinetics, holding potential sensitivity and sensitivity to calcium channel agonists and antagonists.
Calcium channels are multisubunit proteins that contain two large subunits, designated xcex11 and xcex12, which have molecular weights between about 130 and about 200 kilodaltons (xe2x80x9ckDxe2x80x9d), and one to three different smaller subunits of less than about 60 kD in molecular weight. At least one of the larger subunits and possibly some of the smaller subunits are glycosylated. Some of the subunits are capable of being phosphorylated. The xcex11 subunit has a molecular weight of about 150 to about 170 kD when analyzed by sodium dodecylsulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) after isolation from mammalian muscle tissue and has specific binding sites for various 1,4-dihydropyridines (DHPs) and phenylalkylamines. Under non-reducing conditions (in the presence of N-ethylmaleimide), the xcex12 subunit migrates in SDS-PAGE as a band corresponding to a molecular weight of about 160-190 kD. Upon reduction, a large fragment and smaller fragments are released. The xcex2 subunit of the rabbit skeletal muscle calcium channel is a phosphorylated protein that has a molecular weight of 52-65 kD as determined by SDS-PAGE analysis. This subunit is insensitive to reducing conditions. The xcex3 subunit of the calcium channel appears to be a glycoprotein with an apparent molecular weight of 30-33 kD, as determined by SDS-PAGE analysis.
In order to study calcium channel structure and function, large amounts of pure channel protein are needed. Because of the complex nature of these multisubunit proteins, the varying concentrations of calcium channels in tissue sources of the protein, the presence of mixed populations of calcium channels in tissues, difficulties in obtaining tissues of interest, and the modifications of the native protein that can occur during the isolation procedure, it is extremely difficult to obtain large amounts of highly purified, completely intact calcium channel protein.
Characterization of a particular type of calcium channel by analysis of whole cells is severely restricted by the presence of mixed populations of different types of calcium channels in the majority of cells. Single-channel recording methods that are used to examine individual calcium channels do not reveal any information regarding the molecular structure or biochemical composition of the channel. Furthermore, in performing this type of analysis, the channel is isolated from other cellular constituents that might be important for natural functions and pharmacological interactions.
Characterization of the gene or genes encoding calcium channels provides another means of characterization of different types of calcium channels. The amino acid sequence determined from a complete nucleotide sequence of the coding region of a gene encoding a calcium channel protein represents the primary structure of the protein. Furthermore, secondary structure of the calcium channel protein and the relationship of the protein to the membrane may be predicted based on analysis of the primary structure. For instance, hydropathy plots of the a, subunit protein of the rabbit skeletal muscle calcium channel indicate that it contains four internal repeats, each containing six putative transmembrane regions [Tanabe, T. et al. (1987) Nature 328:313].
Because calcium channels are present in various tissues and have a central role in regulating intracellular calcium ion concentrations, they are implicated in a number of vital processes in animals, including neurotransmitter release, muscle contraction, pacemaker activity, and secretion of hormones and other substances. These processes appear to be involved in numerous human disorders, such as CNS and cardiovascular diseases. Calcium channels, thus, are also implicated in numerous disorders. A number of compounds useful for treating various cardiovascular diseases in animals, including humans, are thought to exert their beneficial effects by modulating functions of voltage-dependent calcium channels present in cardiac and/or vascular smooth muscle. Many of these compounds bind to calcium channels and block, or reduce the rate of, influx of Ca2+ into the cells in response to depolarization of the cell membrane.
The results of studies of recombinant expression of rabbit calcium channel xcex11 subunit-encoding cDNA clones and transcripts of the cDNA clones indicate that the xcex11, subunit forms the pore through which calcium enters cells. The relevance of the barium currents generated in these recombinant cells to the actual current generated by calcium channels containing as one component the respective xcex11 subunits in vivo is unclear. In order to completely and accurately characterize and evaluate different calcium channel types, however, it is essential to examine the functional properties of recombinant channels containing all of the subunits as found in vivo.
In order to conduct this examination and to fully understand calcium channel structure and function, it is critical to identify and characterize as many calcium channel subunits as possible. Also in order to prepare recombinant cells for use in identifying compounds that interact with calcium channels, it is necessary to be able to produce cells that express uniform populations of calcium channels containing defined subunits.
An understanding of the pharmacology of compounds that interact with calcium channels in other organ systems, such as the CNS, may aid in the rational design of compounds that specifically interact with subtypes of human calcium channels to have desired therapeutic effects, such as in the treatment of neurodegenerative and cardiovascular disorders. Such understanding and the ability to rationally design therapeutically effective compounds, however, have been hampered by an inability to independently determine the types of human calcium channels and the molecular nature of individual subtypes, particularly in the CNS, and by the unavailability of pure preparations of specific channel subtypes to use for evaluation of the specificity of calcium channel-effecting compounds. Thus, identification of DNA encoding human calcium channel subunits and the use of such DNA for expression of calcium channel subunits and functional calcium channels would aid in screening and designing therapeutically effective compounds.
DNA encoding human xcex11-subunits, including xcex11A-, xcex11B-, xcex11C-, xcex11D- and xcex11E subunits and splice variants thereof has been described (see, e.g., U.S. Pat. No. 5,429,921, published International PCT application No. PCT/US92/06903, International PCT application No. PCT/US94/09230). These subunits appear to participate in formation of high voltage calcium (HVA) channels, which in addition to one of these xcex11-subunits, includes xcex2 subunit and an xcex12-subunit, including xcex4, which is linked to xcex12 by a disulfide bridge and arises from the same precursor. The distinct biophysical and pharmacological properties of each channel derive primarily form the xcex11-subunit, but are modulated by the ancillary subunits, principally the xcex2 subunits associated with the channel. xcex2-subunits have been shown to increase the peak current amplitude, to shift activation/inactivation curves toward more hyperpolarized potentials and to alter kinetics of activation and inactivation (see, e.g., Lambert et al. (1997) J. Neurosci. 17:6621-6625). The xcex12xcex4 subunit, which is tissue-specific, increases the current generated by any xcex11 subunit and potentiates the stimulatory response of xcex2 subunits.
T-type or LVA Channels
Little is known about the channels that have been designated T-channels or LVA (low voltage activated) channels. In general it is believed that T-type currents do not differ fundamentally from other Ca2+ currents. Like HVA channels, T-type channels are selectively permeable to divalent cations, as long as a minimal concentration of divalent cations is present in the external medium. For LVA (or T-type) currents, this minimal Ca2+ concentration is about 25 xcexcm, and for HVA currents it is about 1 xcexcM. T-type current is reported to saturate with a Kd of about 10 mM Ca2+, which is similar to that reported for HVA currents. The channels, however, appear to exhibit certain differences. They differ in their relative permeability to divalent cations. In general, HVA channels are more permeable to Ba2+ than to Ca2+; T-type are equally or slightly less permeable to Ba2+ than to Ca2+. T-type channels also are believed to exhibit slower activation/inactivation and deactivation kinetics and have been reported to exhibit relatively higher sensitivity to Ni2+. This type of channel is activated near the resting potential of the membrane, and is believed to be responsible for the generation of repetitive firing activity or intrinsic neuronal oscillations and for Ca2+ entry accompanying the spike activity (see, e., Huguenard (1996) Annual Rev. Physiol. 58:329-348). Recent data suggests that, xcex2-subunits identified to date may not be a constitutive T-type channel subunit (see, Lambert et al. (1997) J. Neurosci. 17:6621-6625). The structure of calcium channels that generate the various LVA currents is unknown. None of the xcex11 subunits previously cloned appear to have all properties that have been ascribed to the low voltage-activated T-type (or LVA) channels.
Therefore, it is an object herein, to provide nucleic acid encoding specific calcium channel subunits that have structural and functional properties that differ from the HVA type channels. It is also an object herein to provide nucleic acid encoding channels that have activities that have been ascribed to T-type channels and to provide eukaryotic cells bearing recombinant tissue-specific or subtype-specific calcium channels. It is also an object to provide assays for identification of potentially therapeutic compounds that act as modulators of calcium channel activity, particularly those specific for channels that exhibit properties of human T-type channels and other types of channels.
Isolated and purified nucleic acid fragments that encode calcium channel subunits are provided. DNA encoding xcex11 subunits of a human calcium channel, and RNA, encoding such subunits, made upon transcription of such DNA are provided. In particular, nucleic acid molecules encoding xcex11 subunits of voltage-dependent human calcium channels (VDCCs) type A, type B, type C, type D, type E and type T are provided. Also provided is nucleic acid that encodes an xcex11F-subunit of a calcium channel, parituclarly an animal calcium channel and more particularly a mammalian calcium channel.
Nucleic acid encoding xcex11A, xcex11B, xcex11C, xcex11D, xcex11E and xcex11F subunits is provided. Of particular interest herein is the nucleic acid that encodes the xcex11F subunits of calcium channels, particularly mammalian calcium channels. Nucleic acid encoding an exemplary xcex11F subunit is set forth in SEQ ID No. 49. This nucleic acid can be used to isolate minor variants, including splice variants of the nucleic acid encoding xcex11F subunits and allelic variants. Such nucleic acid includes DNA encoding an xcex11F subunit that has substantially the same sequence of amino acids as encoded by the DNA set forth in SEQ ID No. 49. This nucleic acid can also be used to isolate DNA encoding xcex11F subunits from other species, particularly other mammals. Also included are any subunits that are encoded by nucleic acid comprising nucleotides nt 1506 to nt 2627 of SEQ ID No. 49 or subunits that are encoded by nucleic acid that hybridizes to a probe derived from this region.
The xcex11F subunit differs from the xcex11A-xcex11E calcium channel subunits in a number of aspects. First, the intracellular loop positioned between transmembrane Domains I and II is considerably longer than HVA calcium channels. For instance, as exemplified in SEQ ID No. 49 and described below, the intracellular loop between Domains I and II is greater than 1,100 nt (1122 nt), whereas the corresponding region in HVA calcium channels ranges from 351 to 381 nt in length. Thus, the intracellular loop of xcex11F contains approximately 370 additional amino acid residues (aa 420 to aa 794 of SEQ ID No. 50) not found in HVA calcium channel xcex11 subunits. In addition, the encoded amino acid sequence of this loop region is highly proline rich and contains a poly-HIS region of 9 consecutive histidine residues.
Other distinguishing features of the xcex11F subunit, include the absence of amino acid residues in the intracellular loop between transmembrane Domains I and II that are known to be critical (e.g., see De Waard et al. (1996) FEBS Letters 380:272-276; Pragnell et al. (1994) Nature 368:67-70) for the interaction between an xcex11 subunit and a xcex2 subunit. The xcex11F subunit also contains a notably large extracellular loop in Domain I between ISS and IS6. The HVA xcex11 calcium channel subunits provided herein contain 249-270 nucleotide residues in this loop. In contrast, the human xcex11F subunit contains 426 nucleotide residues in this loop. The intracellular loop between transmembrane Domains III and IV is also slightly larger than the HVA xcex11 subunits (186 nt compared to 159-165 nt).
Nucleic acid encoding an xcex11D subunit that includes the amino acids substantially as set forth as residues 10-2161 of SEQ ID No. 1 is also provided. DNA encoding an xcex11D subunit that includes substantially the amino acids set forth as amino acids 1-34 in SEQ ID No. 2 in place of amino acids 373-406 of SEQ ID No. 1 is also provided. DNA encoding an xcex11C subunit that includes the amino acids substantially as set forth in SEQ ID No. 3 or SEQ ID No. 6 and DNA encoding an xcex11B subunit that includes an amino acid sequence substantially as set forth in SEQ ID No. 7 or in SEQ ID No. 8 is also provided.
Nucleic acid encoding xcex11A subunits is also provided. Such DNA includes DNA encoding an xcex11A subunit that has substantially the same sequence of amino acids as encoded by the DNA set forth in SEQ ID No. 22 or No. 23 or other splice variants of xcex11A that include all or part of the sequence set forth in SEQ ID No. 22 or 23. The sequence set forth in SEQ ID NO. 22 is a splice variant designated xcex11A-1; and the sequence set forth in SEQ ID NO. 23 is a splice variant designated xcex11A-2. DNA encoding xcex11A subunits also include DNA encoding subunits that can be isolated using all or a portion of the DNA having SEQ ID NO. 21, 22 or 23 or DNA obtained from the phage lysate of an E. coli host containing DNA encoding an xcex11A subunit that has been deposited in the American Type Culture Collection, 12301 Parklawn Drive, Rockville, Md. 20852 U.S.A. under Accession No. 75293 in accord with the Budapest Treaty. The DNA in such phage includes a DNA fragment having the sequence set forth in SEQ ID No. 21. This fragment selectively hybridizes under conditions of high stringency to DNA encoding xcex11A but not to DNA encoding xcex11B and, thus, can be used to isolate DNA that encodes xcex11A subunits.
Nucleic acid encoding xcex11E subunits of a human calcium channel is also provided. This DNA includes DNA that encodes an xcex11E splice variant designated xcex11E-1 encoded by the DNA set forth in SEQ ID No. 24, and a variant designated xcex11E-3 encoded by SEQ ID No. 25. This DNA also includes other splice variants thereof that encodes sequences of amino acids encoded by all or a portion of the sequences of nucleotides set forth in SEQ ID Nos. 24 and 25 and DNA that hybridizes under conditions of high stringency to the DNA of SEQ ID. No. 24 or 25 and that encodes an xcex11E splice variant.
DNA encoding xcex12B subunits of a human calcium channel, and RNA encoding such subunits, made upon transcription of such a DNA are provided. DNA encoding splice variants of the xcex12 subunit, including tissue-specific splice variants, are also provided. In particular, DNA encoding the xcex12a-xcex12e subunit subtypes is provided. In particularly preferred embodiments, the DNA encoding the xcex12 subunit that is produced by alternative processing of a primary transcript that includes DNA encoding the amino acids set forth in SEQ ID 11 and the DNA of SEQ ID No. 13 inserted between nucleotides 1624 and 1625 of SEQ ID No. 11 is provided. The DNA and amino acid sequences of xcex12a-xcex12e are set forth in SEQ ID Nos. 11 (xcex12b), 29 (xcex12a) and 30-32 (xcex12c-xcex12e, respectively), respectively. RNA encoding these subunits is also provided.
Isolated and purified DNA fragments encoding human calcium channel xcex2 subunits, including DNA encoding xcex21, xcex22, xcex23 and xcex24 subunits, and splice variants of the xcex2 subunits are provided. RNA encoding xcex2 subunits, made upon transcription of the DNA is also provided.
DNA encoding a xcex21 subunit that is produced by alternative processing of a primary transcript that includes DNA encoding the amino acids set forth in SEQ ID No. 9, but including the DNA set forth in SEQ ID No. 12 inserted in place of nucleotides 615-781 of SEQ ID No. 9 is also provided. DNA encoding xcex21 subunits that are encoded by transcripts that have the sequence set forth in SEQ ID No. 9 including the DNA set forth in SEQ ID No. 12 inserted in place of nucleotides 615-781 of SEQ ID No. 9, but that lack one or more of the following sequences of nucleotides: nucleotides 14-34 of SEQ ID No. 12, nucleotides 13-34 of SEQ ID No. 12, nucleotides 35-55 of SEQ ID No. 12, nucleotides 56-190 of SEQ ID No. 12 and nucleotides 191-271 of SEQ ID No. 12 are also provided. In particular, xcex21 subunit splice variants xcex21-1-xcex21-5 (see, SEQ ID Nos. 9, 10 and 33-35) described below, are provided.
xcex22 subunit splice variants xcex22c-xcex22e, that include all or a portion of SEQ ID Nos. 26, 37 and 38 are provided; xcex23 subunit splice variants, including xcex23 subunit splice variants that have the sequences set forth in SEQ ID Nos 19 and 20, and DNA encoding the xcex24 subunit that includes DNA having the sequence set forth in SEQ ID No. 27 and the amino acid sequence set forth in SEQ ID No. 28 are provided.
Also Escherichia coli (E. coil) host cells harboring plasmids containing DNA encoding xcex23 have been deposited in accord with the Budapest Treaty under Accession No. 69048 at the American Type Culture Collection. The deposited clone encompasses nucleotides 122-457 in SEQ ID No. 19 and 112-447 in SEQ ID No. 20.
DNA encoding xcex2 subunits that are produced by alternative processing of a primary transcript encoding a xcex2 subunit, including a transcript that includes DNA encoding the amino acids set forth in SEQ ID No. 9 or including a primary transcript that encodes xcex23 as deposited under ATCC Accession No. 69048, but lacking and including alternative exons are provided or may be constructed from the DNA provided herein.
DNA encoding xcex3 subunits of human calcium channels is also provided. RNA, encoding xcex3 subunits, made upon transcription of the DNA are also provided. In particular, DNA containing the sequence of nucleotides set forth in SEQ ID No. 14 is provided.
Full-length DNA clones and corresponding RNA transcripts, encoding xcex11, including splice variants of xcex11A, xcex11B, xcex11C, xcex11D, and xcex11E, xcex12 and xcex2 subunits, including xcex21-1-xcex21-5, xcex22C, xcex22D, xcex22E, xcex23-1 and xcex24 of human calcium channels are provided. Also provided are DNA clones encoding substantial portions of the certain xcex11C subtype subunits and xcex3 subunits of voltage-dependent human calcium channels for the preparation of full-length DNA clones encoding the corresponding full-length subunits. Full-length clones may be readily obtained using the disclosed DNA as a probe as described herein.
The xcex11F subunit and splice variants thereof and nucleic acids encoding these subunits are of particular interest herein.
Eukaryotic cells containing heterologous DNA encoding one or more calcium channel subunits, particularly human calcium channel subunits, or containing RNA transcripts of DNA clones encoding one or more of the subunits are provided. A single xcex11 subunit can form a channel. The requisite combination of subunits for formation of active channels in selected cells, however, can be determined empirically using the methods herein. For example, if a selected xcex11 subtype or variant does not form an active channel in a selected cell line, an additional subunit or subunits can be added until an active channel is formed.
In preferred embodiments, the cells contain DNA or RNA encoding an xcex11 subunit, preferably an xcex11F subunit of an animal, preferably of a mammalian calcium channel. Embodiments in which the cells contain nucleic acid encoding an xcex11F are of particular interest herein. In more preferred embodiments, the cells contain DNA or RNA encoding additional heterologous subunits, including an xcex12xcex4. The cells may also include nucleic acid encoding a xcex2 subunit and/or a xcex3 subunit. In such embodiments, eukaryotic cells stably or transiently transfected with any combination of one, two, three or four of the subunit-encoding DNA clones, such as DNA encoding any of xcex11, xcex11+xcex2, xcex11+xcex2+xcex12, are provided. The eukaryotic cells provided herein contain heterologous nucleic acid that encodes an xcex11 subunit and optionally a heterologous xcex12-subunit and/or a xcex2 subunit and/or xcex3 subunit.
In preferred embodiments, the cells express such heterologous calcium channel subunits and include one or more of the subunits in membrane-spanning heterologous calcium channels. In more preferred embodiments, the eukaryotic cells express functional, heterologous calcium channels that are capable of gating the passage of calcium channel-selective ions and/or binding compounds that, at physiological concentrations, modulate the activity of the heterologous calcium channel. In certain embodiments, the heterologous calcium channels include at least one heterologous calcium channel subunit. In most preferred embodiments, the calcium channels that are expressed on the surface of the eukaryotic cells are composed substantially or entirely of subunits encoded by the heterologous DNA or RNA. In preferred embodiments, the heterologous calcium channels of such cells are distinguishable from any endogenous calcium channels of the host cell. Such cells provide a means to obtain homogeneous populations of calcium channels. Typically, the cells contain the selected calcium channel as the only heterologous ion channel expressed by the cell.
In certain embodiments the recombinant eukaryotic cells that contain the heterologous DNA encoding the calcium channel subunits are produced by transfection with DNA encoding one or more of the subunits or are injected with RNA transcripts of DNA encoding one or more of the calcium channel subunits. The DNA may be introduced as a linear DNA fragment or may be included in an expression vector for stable or transient expression of the subunit-encoding DNA. Vectors containing DNA encoding human calcium channel subunits are also provided.
The eukaryotic cells that express heterologous calcium channels may be used in assays for calcium channel function or, in the case of cells transformed with fewer subunit-encoding nucleic acids than necessary to constitute a functional recombinant human calcium channel, such cells may be used to assess the effects of additional subunits on calcium channel activity. The additional subunits can be provided by subsequently transfecting such a cell with one or more DNA clones or RNA transcripts encoding human calcium channel subunits.
The recombinant eukaryotic cells that express membrane spanning heterologous calcium channels may be used in methods for identifying compounds that modulate calcium channel activity. In particular, the cells are used in assays that identify agonists and antagonists of calcium channel activity in humans and/or assessing the contribution of the various calcium channel subunits to the transport and regulation of transport of calcium ions. Because the cells constitute homogeneous populations of calcium channels, they provide a means to identify agonists or antagonists of calcium channel activity that are specific for each such population.
The assays that use the eukaryotic cells for identifying compounds that modulate calcium channel activity are also provided. In practicing these assays the eukaryotic cell that expresses a heterologous calcium channel, containing at least one subunit encoded by the DNA provided herein, is in a solution containing a test compound and a calcium channel selective ion, the cell membrane is depolarized, and current flowing into the cell is detected. If the test compound is one that modulates calcium channel activity, the current that is detected is different from that produced by depolarizing the same or a substantially identical cell in the presence of the same calcium channel-selective ion but in the absence of the compound. In preferred embodiments, prior to the depolarization step, the cell is maintained at a holding potential which substantially inactivates calcium channels which are endogenous to the cell. Also in preferred embodiments, the cells are mammalian cells, most preferably HEK cells, or amphibian oxc3x6cytes.
Transcription based assays for identifying compounds that modulate the activity of calcium channels (see, U.S. Pat. Nos. 5,436,128 and 5,401,629), particularly calcium channels that contain an xcex11F subunit are provided. These assays use cells that express calcium channels, particularly calcium channels containing an xcex11F-subunit, and more preferably an xcex11F-subunit encoded by heterologous DNA, and also contain nucleic acid encoding a reporter gene construct containing a reporter gene in operative linkage with one or more transcriptional control elements that is regulated by a calcium channel. The assays are effected by comparing the difference in the amount of transcription of a the reporter gene in the cells provided herein in the presence of the compound with the amount of transcription in the absence of the compound, or with the amount of transcription in the absence of the heterologous calcium channel, whereby compounds that modulate the activity of the heterologous calcium channel in the cell are identified. The reporter gene is any such gene known to those of skill in the art, including, but not limited to the gene encoding bacterial chloramphenicol acetyltransferase, the gene encoding firefly luciferase, the gene encoding bacterial luciferase, the gene encoding xcex2-galactosidase or the gene encoding alkaline phosphatase, and the transcriptional control element is any such element known to those of skill in the art, including, but not limited to serum responsive elements, cyclic adenosine monophosphate responsive elements, the c-fos gene promoter, the vasoactive intestinal peptide gene promoter, the somatostatin gene promoter, the proenkephalin promoter, the phosphoenolpyruvate carboxykinase gene promoter or the nerve growth factor-1 A gene promoter and elements responsive to intracellular calcium ion levels.
Nucleic acid probes can be labeled, which if needed, for detection, containing at least about 14, preferably 16, or, if desired, 20 or 30 or more, contiguous nucleotides of xcex11D, xcex11C, xcex11B, xcex11A, xcex11E, xcex11F, xcex12xcex4, xcex2, including xcex21, xcex22, xcex23 and xcex24 and xcex3 subunit-encoding nucleic acids and splice variants are provided. Methods using the probes for the isolation and cloning of calcium channel subunit-encoding DNA, including splice variants within tissues and inter-tissue variants are also provided.
Other assays in which receptor activity in response to test compounds is measured may also be practiced with the cells provided herein (see, e.g., U.S. Pat. No. 5,670,113).
Purified human calcium channel subunits and purified human calcium channels are provided. The subunits and channels can be isolated from a eukaryotic cell transfected with DNA that encodes the subunit.
In another embodiment, immunoglobulins or antibodies obtained from the serum of an animal immunized with a substantially pure preparation of a human calcium channel, human calcium channel subunit or epitope-containing fragment of a human calcium subunit are provided. Monoclonal antibodies produced using a human calcium channel, human calcium channel subunit or epitope-containing fragment thereof as an immunogen are also provided. E. coli fusion proteins including a fragment of a human calcium channel subunit may also be used as immunogen. Such fusion proteins may contain a bacterial protein or portion thereof, such as the E. coil TrpE protein, fused to a calcium channel subunit peptide. The immunoglobulins that are produced using the calcium channel subunits or purified calcium channels as immunogens have, among other properties, the ability to specifically and preferentially bind to and/or cause the immunoprecipitation of a human calcium channel or a subunit thereof which may be present in a biological sample or a solution derived from such a biological sample. Such antibodies may also be used to selectively isolate cells that express calcium channels that contain the subunit for which the antibodies are specific.
Methods for modulating the activity of ion channels by contacting the calcium channels with an effective amount of the above-described antibodies are also provided.
Definitions:
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which this invention belongs. All patents and publications referred to herein are incorporated by reference herein.
Reference to each of the calcium channel subunits includes the subunits that are specifically disclosed herein and human calcium channel subunits encoded by nucleic acid that can be isolated by using the nucleic acid disclosed as probes and screening an appropriate human cDNA or genomic library under at least low stringency. Such DNA also includes DNA that encodes proteins that have about 40% homology to any of the subunits proteins described herein or DNA that hybridizes under conditions of at least low stringency to the DNA provided herein and the protein encoded by such DNA exhibits additional identifying characteristics, such as function or molecular weight. In particular, reference to an xcex11F subunit refers to subunits that can be isolated from nucleic acid libraries from any desired source using the nucleic acid disclosed herein as a probe. The encoded subunit is characterized by the presence of the notably long intracellular loop between transmembrane domains I and II, and/or properties ascribed to T-type or LVA type channels.
It is understood that subunits that are encoded by transcripts that represent splice variants of the disclosed subunits or other such subunits may exhibit less than 40% overall homology to any single subunit, but will include regions of such homology to one or more such subunits. It is also understood that 40% homology refers to proteins that share approximately 40% of their amino acids in common or that share somewhat less, but include conservative amino acid substitutions, whereby the activity of the protein is not substantially altered.
The subunits and DNA fragments encoding such subunits provided herein include any xcex11, xcex12, xcex2 or xcex3 subunits of a human calcium channel. In particular, such DNA fragments include any isolated DNA fragment that (encodes a subunit of a human calcium channel, that (1) contains a sequence of nucleotides that encodes the subunit, and (2) is selected from among:
(a) a sequence of nucleotides that encodes a human calcium channel subunit and includes a sequence of nucleotides set forth in any of the SEQ ID""s herein (i.e., SEQ ID Nos. 1-52) that encodes such subunit;
(b) a sequence of nucleotides that encodes the subunit and hybridizes under conditions of high stringency to DNA that is complementary to an mRNA transcript present in a human cell that encodes a subunit that includes the sequence of nucleotides set forth in any of SEQ ID No. 1-52;
(c) a sequence of nucleotides that encodes the subunit that includes a sequence of amino acids encoded by any of SEQ ID Nos. 1-52; and
(d) a sequence of nucleotides that encodes a subunit that includes a sequence of amino acids encoded by a sequence of nucleotides that encodes such subunit and hybridizes under conditions of high stringency to DNA that is complementary to an mRNA transcript present in a human cell that encodes the subunit that includes the sequence of nucleotides set forth in any of SEQ ID Nos. 1-52.
As used herein, the xcex11 subunit types, encoded by different genes, are designated as type xcex11A, xcex11B, xcex11C, xcex11D, xcex11E and xcex11F. These types have also been referred to as VDCC IV for xcex11B, VDCC II for xcex11C and VDCC III for xcex11D. Subunit subtypes, which are splice variants, are referred to, for example as xcex11B-1, xcex11B-2, xcex11C-1 etc.
Thus, as used herein, DNA encoding the xcex11 subunit refers to DNA that hybridizes to the DNA provided herein under conditions of at least low stringency or encodes a subunit that has at least about 40% homology to protein encoded by DNA disclosed herein that encodes an xcex11 subunit of a human calcium channel. In particular, a splice variant of any of the xcex11 subunits (or any of the subunits particularly disclosed herein) will contain regions (at least one exon) of divergence and one or more regions (at least one exon, typically more than about 16 nucleotides, and generally substantially more) that have 100% homology with one or more of the xcex11 subunit subtypes provided herein, and will also contain a region that has substantially less homology, since it is derived from a different exon. It is well within the skill of those in this art to identify exons and splice variants. Thus, for example, an xcex11A subunit will be readily identifiable, because it will share at least about 40% protein homology with one of the xcex11A subunits disclosed herein, and will include at least one region (one exon) that is 100% homologous. It will also have activity, as discussed below, that indicates that it is an xcex11 subunit.
An xcex11 subunit may be identified by its ability to form a calcium channel. Typically, xcex11 subunits have molecular masses greater than at least about 120 kD. Also, hydropathy plots of deduced xcex11 subunit amino acid sequences indicate that the xcex11 subunits contain four internal repeats, each containing six putative transmembrane domains.
The activity of a calcium channel may be assessed in vitro by methods known to those of skill in the art, including the electrophysiological and other methods described herein. Typically, xcex11 subunits include regions with which one or more modulators of calcium channel activity, such as a 1,4-DHP or xcfx89-CgTx, interact directly or indirectly. Types of xcex11 subunits may be distinguished by any method known to those of skill in the art, including on the basis of binding specificity. For example, it has been found herein that xcex11B subunits participate in the formation of channels that have previously been referred to as N-type channels, xcex11D subunits participate in the formation of channels that had previously been referred to as L-type channels, xcex11A subunits appear to participate in the formation of channels that exhibit characteristics typical of channels that had previously been designated P-type channels, and xcex11F subunits appear to participate in channels that exhibit activities associated with T-type channels. Thus, for example, the activity of channels that contain the xcex11B subunit are insensitive to 1,4-DHPs; whereas the activity of channels that contain the xcex11D subunit are modulated or altered by a 1,4-DHP. It is presently preferable to refer to calcium channels based on pharmacological characteristics and current kinetics and to avoid historical designations. Types and subtypes of xcex11 subunits may be characterized on the basis of the effects of such modulators on the subunit or a channel containing the subunit as well as differences in currents and current kinetics produced by calcium channels containing the subunit. The xcex11F subunits may be further identified by the presence the notably long intracellular loop regions, such as between transmembrane domains I and II (e.g., nt 1506 to nt 2627 of SEQ ID No. 49), and also the loop in domain I.
As used herein, an xcex12 subunit is encoded by DNA that hybridizes to the DNA provided herein under conditions of low stringency or encodes a protein that has at least about 40% homology with that disclosed herein. Such DNA encodes a protein that typically has a molecular mass greater than about 120 kD, but does not form a calcium channel in the absence of an xcex11 subunit, and may alter the activity of a calcium channel that contains an xcex11 subunit. Subtypes of the xcex12 subunit that arise as splice variants are designated by lower case letter, such as xcex12a . . . xcex12e. In addition, the xcex12 subunit and the large fragment produced when the protein is subjected to reducing conditions appear to be glycosylated with at least N-linked sugars and do not specifically bind to the 1,4-DHPs and phenylalkylamines that specifically bind to the xcex11 subunit. The smaller fragment, the C-terminal fragment, is referred to as the xcex4 subunit and includes amino acids from about 946 (SEQ ID No. 11) through about the C-terminus. This fragment may dissociate from the remaining portion of xcex12 when the xcex12 subunit is exposed to reducing conditions. For purposes herein xcex12 is also referred to as xcex12xcex4. Thus, reference to xcex12xcex4 means the xcex12 subunit, including the C-terminal xcex4 portion.
As used herein, a xcex2 subunit is encoded by DNA that hybridizes to the DNA provided herein under conditions of low stringency or encodes a protein that has at least about 40% homology with that disclosed herein and is a protein that typically has a molecular mass lower than the a subunits and on the order of about 50-80 kD, does not form a detectable calcium channel in the absence of an xcex11 subunit, but may alter the activity of a calcium channel that contains an xcex11 subunit or that contains an xcex11 and xcex12 subunit.
Types of the xcex2 subunit that are encoded by different genes are designated with subscripts, such as xcex21, xcex22, xcex23 and xcex24. Subtypes of xcex2 subunits that arise as splice variants of a particular type are designated with a numerical subscript referring to the type and to the variant. Such subtypes include, but are not limited to the xcex21 splice variants, including xcex21-1-xcex21-5 and xcex22 variants, including xcex22C-xcex22E.
As used herein, a xcex3 subunit is a subunit encoded by DNA disclosed herein as encoding the xcex3 subunit and may be isolated and identified using the DNA disclosed herein as a probe by hybridization or other such method known to those of skill in the art, whereby full-length clones encoding a xcex3 subunit may be isolated or constructed. A xcex3 subunit will be encoded by DNA that hybridizes to the DNA provided herein under conditions of low stringency or exhibits sufficient sequence homology to encode a protein that has at least about 40% homology with the xcex3 subunit described herein.
Thus, one of skill in the art, in light of the disclosure herein, can identify DNA encoding xcex11, xcex12, xcex2, xcex4 and xcex3 calcium channel subunits, including types encoded by different genes and subtypes that represent splice variants. For example, DNA probes based on the DNA disclosed herein may be used to screen an appropriate library, including a genomic or cDNA library, for hybridization to the probe and obtain DNA in one or more clones that includes an open reading fragment that encodes an entire protein. Subsequent to screening an appropriate library with the DNA disclosed herein, the isolated DNA can be examined for the presence of an open reading frame from which the sequence of the encoded protein may be deduced. Determination of the molecular weight and comparison with the sequences herein should reveal the identity of the subunit as an xcex11, xcex12 etc. subunit. Functional assays may, if necessary, be used to determine whether the subunit is an xcex11, xcex12 subunit or xcex2 subunit.
For example, DNA encoding an xcex11A subunit may be isolated by screening an appropriate library with DNA, encoding all or a portion of the human xcex11A subunit. Such DNA includes the DNA in the phage deposited under ATCC Accession No. 75293 that encodes a portion of an xcex11 subunit. DNA encoding an xcex11A subunit may be obtained from an appropriate library by screening with an oligonucleotide having all or a portion of the sequence set forth in SEQ ID No. 21, 22 and/or 23 or with the DNA in the deposited phage. Alternatively, such DNA may have a sequence that encodes an xcex11A subunit that is encoded by SEQ ID NO. 22 or 23.
Similarly, DNA encoding xcex23 may be isolated by screening a human cDNA library with DNA probes prepared from the plasmid xcex21.42 deposited under ATCC Accession No. 69048 or may be obtained from an appropriate library using probes having sequences prepared according to the sequences set forth in SEQ ID Nos. 19 and/or 20. Also, DNA encoding xcex24 may be isolated by screening a human cDNA library with DNA probes prepared according to DNA set forth in SEQ ID No. 27, which sets forth the DNA sequence of a clone encoding a xcex24 subunit. The amino acid sequence is set forth in SEQ ID No. 28. Any method known to those of skill in the art for isolation and identification of DNA and preparation of full-length genomic or cDNA clones, including methods exemplified herein, may be used.
The subunit encoded by isolated DNA may be identified by comparison with the DNA and amino acid sequences of the subunits provided herein. Splice variants share extensive regions of homology, but include non-homologous regions, subunits encoded by different genes share a uniform distribution of non-homologous sequences.
As used herein, a splice variant refers to a variant produced by differential processing of a primary transcript of genomic DNA that results in more than one type of mRNA. Splice variants may occur within a single tissue type or among tissues (tissue-specific variants). Thus, cDNA clones that encode calcium channel subunit subtypes that have regions of identical amino acids and regions of different amino acid sequences are referred to herein as xe2x80x9csplice variantsxe2x80x9d.
As used herein, a xe2x80x9ccalcium channel-selective ionxe2x80x9d is an ion that is capable of flowing through, or being blocked from flowing through, a calcium channel which spans a cellular membrane under conditions which would substantially similarly permit or block the flow of Ca2+. Ba2+ is an example of an ion which is a calcium channel-selective ion.
As used herein, a compound that modulates calcium channel activity is one that affects the ability of the calcium channel to pass calcium channel-selective ions or affects other detectable calcium channel features, such as current kinetics. Such compounds include calcium channel antagonists and agonists and compounds that exert their effect on the activity of the calcium channel directly or indirectly.
As used herein, a xe2x80x9csubstantially purexe2x80x9d subunit or protein is a subunit or protein that is sufficiently free of other polypeptide contaminants to appear homogeneous by SDS-PAGE or to be unambiguously sequenced.
As used herein, selectively hybridize means that a DNA fragment hybridizes to a second fragment with sufficient specificity to permit the second fragment to be identified or isolated from among a plurality of fragments. In general, selective hybridization occurs at conditions of high stringency.
As used herein, heterologous or foreign DNA and RNA are used interchangeably and refer to DNA or RNA that does not occur naturally as part of the genome in which it is present or which is found in a location or locations in the genome that differ from that in which it occurs in nature. It is DNA or RNA that is not endogenous to the cell and has been artificially introduced into the cell. Examples of heterologous DNA include, but are not limited to, DNA that encodes a calcium channel subunit and DNA that encodes RNA or proteins that mediate or alter expression of endogenous DNA by affecting transcription, translation, or other regulatable biochemical processes. The cell that expresses the heterologous DNA, such as DNA encoding a calcium channel subunit, may contain DNA encoding the same or different calcium channel subunits. The heterologous DNA need not be expressed and may be introduced in a manner such that it is integrated into the host cell genome or is maintained episomally.
As used herein, operative linkage of heterologous DNA to regulatory and effector sequences of nucleotides, such as promoters, enhancers, transcriptional and translational stop sites, and other signal sequences, refers to the functional relationship between such DNA and such sequences of nucleotides. For example, operative linkage of heterologous DNA to a promoter refers to the physical and functional relationship between the DNA and the promoter such that the transcription of such DNA is initiated from the promoter by an RNA polymerase that specifically recognizes, binds to and transcribes the DNA in reading frame.
As used herein, isolated, substantially pure DNA refers to DNA fragments purified according to standard techniques employed by those skilled in the art [see, e.g., Maniatis et al. (1982) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.].
As used herein, expression refers to the process by which nucleic acid is transcribed into mRNA and translated into peptides, polypeptides, or proteins. If the nucleic acid is derived from genomic DNA, expression may, if an appropriate eukaryotic host cell or organism is selected, include splicing of the mRNA.
As used herein, vector or plasmid refers to discrete elements that are used to introduce heterologous DNA into cells for either expression of the heterologous DNA or for replication of the cloned heterologous DNA. Selection and use of such vectors and plasmids are well within the level of skill of the art.
As used herein, expression vector includes vectors capable of expressing DNA fragments that are in operative linkage with regulatory sequences, such as promoter regions, that are capable of effecting expression of such DNA fragments. Thus, an expression vector refers to a recombinant DNA or RNA construct, such as a plasmid, a phage, recombinant virus or other vector that, upon introduction into an appropriate host cell, results in expression of the cloned DNA. Appropriate expression vectors are well known to those of skill in the art and include those that are replicable in eukaryotic cells and/or prokaryotic cells and those that remain episomal or may integrate into the host cell genome.
As used herein, a promoter region refers to the portion of DNA of a gene that controls transcription of the DNA to which it is operatively linked. The promoter region includes specific sequences of DNA that are sufficient for RNA polymerase recognition, binding and transcription initiation. This portion of the promoter region is referred to as the promoter. In addition, the promoter region includes sequences that modulate this recognition, binding and transcription initiation activity of the RNA polymerase. These sequences may be cis acting or may be responsive to trans acting factors. Promoters, depending upon the nature of the regulation, may be constitutive or regulated.
As used herein, a recombinant eukaryotic cell is a eukaryotic cell that contains heterologous DNA or RNA.
As used herein, a recombinant or heterologous calcium channel refers to a calcium channel that contains one or more subunits that are encoded by heterologous DNA that has been introduced into and expressed in a eukaryotic cell that expresses the recombinant calcium channel. A recombinant calcium channel may also include subunits that are produced by DNA endogenous to the cell. In certain embodiments, the recombinant or heterologous calcium channel may contain only subunits that are encoded by heterologous DNA.
As used herein, xe2x80x9cfunctionalxe2x80x9d with respect to a recombinant or heterologous calcium channel means that the channel is able to provide for and regulate entry of calcium channel-selective ions, including, but not limited to, Ca2+ or Ba2+, in response to a stimulus and/or bind ligands with affinity for the channel. Preferably such calcium channel activity is distinguishable, such as by electrophysiological, pharmacological and other means known to those of skill in the art, from any endogenous calcium channel activity that is in the host cell.
As used herein, a T-type channel or LVA type channel typically refers to a calcium channel that exhibits a low-threshold calcium current that is activated and inactivated at low voltages compared to calcium channels (such as those that include an xcex11D subunit) referred to as high voltage activated (HVA) channels. In addition or alternatively, a T-type channel may be characterized by distinct biophysical features, such as slow deactivation rates, very low conductances (5-9 pS) and voltage-dependent inactivation. T channels may exhibit a relatively high degree of sensitivity to mibefradil and/or a relatively high degree of resistance to the Conus snail toxins GVIA and MVIIC as well as the arachnid toxins AgaIIIA and AgaIVA compared to HVA calcium channels. These channels also typically exhibit reduced affinity for cadmium. T-type channels or LVA type channels may also be characterized at the nucleic acid level by the presence of one or more extended intracellular loop (see, e.g., SEQ ID NO. 49) between transmembrane domains, such as between transmembrane domains I and II.
As used herein, a peptide having an amino acid sequence substantially as set forth in a particular SEQ ID No. 51 and 52 includes peptides that may have the same function but may include minor variations in sequence, such as conservative amino acid changes or minor deletions or insertions that do not alter the activity of the peptide. The activity of a calcium channel receptor subunit peptide refers to its ability to form functional calcium channels with other such subunits.
As used herein, a physiological concentration of a compound is that which is necessary and sufficient for a biological process to occur. For example, a physiological concentration of a calcium channel-selective ion is a concentration of the calcium channel-selective ion necessary and sufficient to provide an inward current when the channels open.
As used herein, activity of a calcium channel refers to the movement of a calcium channel-selective ion through a calcium channel. Such activity may be measured by any method known to those of skill in the art, including, but not limited to, measurement of the amount of current which flows through the recombinant channel in response to a stimulus.
As used herein, a xe2x80x9cfunctional assayxe2x80x9d refers to an assay that identifies functional calcium channels. A functional assay, thus, is an assay to assess function.
As understood by those skilled in the art, assay methods for identifying compounds, such as antagonists and agonists, that modulate calcium channel activity, generally require comparison to a control. One type of a xe2x80x9ccontrolxe2x80x9d cell or xe2x80x9ccontrolxe2x80x9d culture is a cell or culture that is treated substantially the same as the cell or culture exposed to the test compound except that the control culture is not exposed to the test compound. Another type of a xe2x80x9ccontrolxe2x80x9d cell or xe2x80x9ccontrolxe2x80x9d culture may be a cell or a culture of cells which are identical to the transfected cells except the cells employed for the control culture do not express functional calcium channels. In this situation, the response of test cell to the test compound is compared to the response (or lack of response) of the calcium channel-negative cell to the test compound, when cells or cultures of each type of cell are exposed to substantially the same reaction conditions in the presence of the compound being assayed. For example, in methods that use patch clamp electrophysiological procedures, the same cell can be tested in the presence and absence of the test compound, by changing the external solution bathing the cell as known in the art.
It is also understood that each of the subunits disclosed herein may be modified by making conservative amino acid substitutions and the resulting modified subunits are contemplated herein. Suitable conservative substitutions of amino acids are known to those of skill in this art and may be made generally without altering the biological activity of the resulting molecule. Those of skill in this art recognize that, in general, single amino acid substitutions in non-essential regions of a polypeptide do not substantially alter biological activity (see, e.g., Watson et al. Molecular Biology of the Gene, 4th Edition, 1987, The Benjamin/Cummings Pub. Co., p.224). Such substitutions are preferably, although not exclusively, made in accordance with those set forth in TABLE 1 as follows:
Other substitutions are also permissible and may be determined empirically or in accord with known conservative substitutions. Any such modification of the polypeptide may be effected by any means known to those of skill in this art. Mutation may be effected by any method known to those of skill in the art, including site-specific or site-directed mutagenesis of DNA encoding the protein and the use of DNA amplification methods using primers to introduce and amplify alterations in the DNA template.
Identification and Isolation of DNA Encoding Human Calcium Channel Subunits
Methods for identifying and isolating DNA encoding xcex11, xcex12, xcex2 and xcex3 subunits of human calcium channels are provided. Identification and isolation of such DNA may be accomplished by hybridizing, under appropriate conditions, at least low stringency whereby DNA that encodes the desired subunit is isolated, restriction enzyme-digested human DNA with a labeled probe having at least 14, preferably 16 or more nucleotides and derived from any contiguous portion of DNA having a sequence of nucleotides set forth herein by sequence identification number. Once a hybridizing fragment is identified in the hybridization reaction, it can be cloned employing standard cloning techniques known to those of skill in the art. Full-length clones may be identified by the presence of a complete open reading frame and the identity of the encoded protein verified by sequence comparison with the subunits provided herein and by functional assays to assess calcium channel-forming ability or other function. This method can be used to identify genomic DNA encoding the subunit or cDNA encoding splice variants of human calcium channel subunits generated by alternative splicing of the primary transcript of genomic subunit DNA. For instance, DNA, cDNA or genomic DNA, encoding a calcium channel subunit may be identified by hybridization to a DNA probe and characterized by methods known to those of skill in the art, such as restriction mapping and DNA sequencing, and compared to the DNA provided herein in order to identify heterogeneity or divergence in the sequences of the DNA. Such sequence differences may indicate that the transcripts from which the cDNA was produced result from alternative splicing of a primary transcript, if the non-homologous and homologous regions are clustered, or from a different gene if the non-homologous regions are distributed throughout the cloned DNA. Splice variants share regions of 100% homology.
Any suitable method for isolating genes using the DNA provided herein may be used. For example, oligonucleotides corresponding to regions of sequence differences have been used to isolate, by hybridization, DNA encoding the full-length splice variant and can be used to isolate genomic clones. A probe, based on a nucleotide sequence disclosed herein, which encodes at least a portion of a subunit of a human calcium channel, such as a tissue-specific exon, may be used as a probe to clone related DNA, to clone a full-length cDNA clone or genomic clone encoding the human calcium channel subunit.
Labeled, including, but not limited to, radioactively or enzymatically labeled, RNA or single-stranded DNA of at least 14 substantially contiguous bases, preferably 16 or more, generally at least 30 contiguous bases of a nucleic acid which encodes at least a portion of a human calcium channel subunit, the sequence of which nucleic acid corresponds to a segment of a nucleic acid sequence disclosed herein by reference to a SEQ ID No. are provided. Such nucleic acid segments may be used as probes in the methods provided herein for cloning DNA encoding calcium channel subunits. See, generally, Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory Press.
In addition, nucleic acid amplification techniques, which are well known in the art, can be used to locate splice variants of calcium channel subunits by employing oligonucleotides based on DNA sequences surrounding the divergent sequence primers for amplifying human RNA or genomic DNA. Size and sequence determinations of the amplification products can reveal splice variants. Furthermore, isolation of human genomic DNA sequences by hybridization can yield DNA containing multiple exons, separated by introns, that correspond to different splice variants of transcripts encoding human calcium channel subunits.
DNA encoding types and subtypes of each of the xcex11, xcex12, xcex2 and xcex3 subunits of voltage-dependent human calcium channels has been cloned herein by nucleic acid amplication of cDNA from selected tissues or by screening human cDNA libraries prepared from isolated poly A+mRNA from cell lines or tissue of human origin having such calcium channels. Among the sources of such cells or tissue for obtaining mRNA are human brain tissue or a human cell line of neural origin, such as a neuroblastoma cell line, human skeletal muscle or smooth muscle cells, and the like. Methods of preparing cDNA libraries are well known in the art [see generally Ausubel et al. (1987) Current Protocols in Molecular Biology, Wiley-Interscience, New York; and Davis et al. (1986) Basic Methods in Molecular Biology, Elsevier Science Publishing Co., New York].
Preferred regions from which to construct probes include 5xe2x80x2 and/or 3xe2x80x2 coding sequences, sequences predicted to encode transmembrane domains, sequences predicted to encode cytoplasmic loops, signal sequences, ligand-binding sites, and other functionally significant sequences (see Table, below). Either the full-length subunit-encoding DNA or fragments thereof can be used as probes, preferably labeled with suitable label means for ready detection. When fragments are used as probes, preferably the DNA sequences will be typically from the carboxyl-end-encoding portion of the DNA, and most preferably will include predicted transmembrane domain-encoding portions based on hydropathy analysis of the deduced amino acid sequence [see, e.g., Kyte and Doolittle [(1982) J. Mol. Biol. 167:105].
Particularly preferred regions from which to construct probes for the isolation of DNA encoding a human xcex1-1F subunit include the nucleic acid sequence encoding the notably long intracellular loop located between transmembrane Domains I and II (e.g., nt 1506 to nt 2627 of SEQ ID No. 49). Probes for isolating DNA encoding a human xcex1-1F subunit are preferably 14 or 16 contiguous nucleotides in length. In some instances, probes of 30 or 50 nucleotides are preferred and in other instances probes between 50 to 100 nucleotides are preferred.
Riboprobes that are specific for human calcium channel subunit types or subtypes have been prepared. These probes are useful for identifying expression of particular subunits in selected tissues and cells. The regions from which the probes were prepared were identified by comparing the DNA and amino acid sequences of all known xcex1 or xcex2 subunit subtypes. Regions of least homology, preferably human-derived sequences, and generally about 250 to about 600 nucleotides were selected. Numerous riboprobes for xcex1 and xcex2 subunits have been prepared; some of these are listed in the following Table.
The above-noted nucleotide regions are also useful in selecting regions of the protein for preparation of subunit-specific antibodies, discussed below.
The DNA clones and fragments thereof provided herein thus can be used to isolate genomic clones encoding each subunit and to isolate any splice variants by hybridization screening of libraries prepared from different human tissues. Nucleic acid amplification techniques, which are well known in the art, can also be used to locate DNA encoding splice variants of human calcium channel subunits. This is accomplished by employing oligonucleotides based on DNA sequences surrounding divergent sequence(s) as primers for amplifying human RNA or genomic DNA. Size and sequence determinations of the amplification products can reveal the existence of splice variants. Furthermore, isolation of human genomic DNA sequences by hybridization can yield DNA containing multiple exons, separated by introns, that correspond to different splice variants of transcripts encoding human calcium channel subunits.
Once DNA encoding a calcium channel subunit is isolated, ribonuclease (RNase) protection assays can be employed to determine which tissues express mRNA encoding a particular calcium channel subunit or variant. These assays provide a sensitive means for detecting and quantitating an RNA species in a complex mixture of total cellular RNA. The subunit DNA is labeled and hybridized with cellular RNA. If complementary mRNA is present in the cellular RNA, a DNA-RNA hybrid results. The RNA sample is then treated with RNase, which degrades single-stranded RNA. Any RNA-DNA hybrids are protected from RNase degradation and can be visualized by gel electrophoresis and autoradiography. In situ hybridization techniques can also be used to determine which tissues express mRNA encoding a particular calcium channel subunit. The labeled subunit-encoding DNA clones are hybridized to different tissue slices to visualize subunit mRNA expression.
With respect to each of the respective subunits (xcex11, xcex12, xcex2 or xcex3) of human calcium channels, once the DNA encoding the channel subunit was identified by a nucleic acid screening method, the isolated clone was used for further screening to identify overlapping clones. Some of the cloned DNA fragments can and have been subcloned into an appropriate vector such as pIBI24/25 (IBI, New Haven, Conn.), M13mp 18/19, pGEM4, pGEM3, pGEM7Z, pSP72 and other such vectors known to those of skill in this art, and characterized by DNA sequencing and restriction enzyme mapping. A sequential series of overlapping clones may thus be generated for each of the subunits until a full-length clone can be prepared by methods, known to those of skill in the art, that include identification of translation initiation (start) and translation termination (stop) codons. For expression of the cloned DNA, the 5xe2x80x2 noncoding region and other transcriptional and translational control regions of such a clone may be replaced with an efficient ribosome binding site and other regulatory regions as known in the art. Other modifications of the 5xe2x80x2 end, known to those of skill in the art, that may be required to optimize translation and/or transcription efficiency may also be effected, if deemed necessary.
Examples II-VIII, below, describe in detail the cloning of each of the various subunits of a human calcium channel as well as subtypes and splice variants, including tissue-specific variants thereof. In the few instances in which partial sequences of a subunit are disclosed, it is well within the skill of the art, in view of the teaching herein, to obtain the corresponding full-length clones and sequence thereof encoding the subunit, subtype or splice variant thereof using the methods described above and exemplified below.
Identification and Isolation of DNA Encoding Additional xcex11 Human Calcium Channel Subunit Types and Subtypes
DNA encoding additional xcex11 subunits can be isolated and identified using the DNA provided herein as described for the xcex11A, xcex11B, xcex11C, xcex11D, xcex11E and xcex11F subunits or using other methods known to those of skill in the art. In particular, the DNA provided herein may be used to screen appropriate libraries to isolate related DNA. Full-length clones can be constructed using methods, such as those described herein, and the resulting subunits characterized by comparison of their sequences and electrophysiological and pharmacological properties with the subunits exemplified herein.
A number of voltage-dependent calcium channel xcex11 subunit genes, which are expressed in the human CNS and in other tissues, have been identified and have been designated as xcex11A, xcex11B (or VDCC IV), xcex11C (or VDCC II), xcex11D (or VDCC II), xcex11E and xcex11F. DNA, isolated from a human DNA libraries that encodes each of the subunit types has been isolated. DNA encoding subtypes of each of the types, which arise as splice variants are also provided. Subtypes are herein designated, for example, as xcex11B-1, xcex11B-2. The xcex11F subunit is of particular interest herein
The xcex11, subunit types A, B, C, D, E and F of voltage-dependent calcium channels, and subtypes thereof, differ with respect to sensitivity to known classes of calcium channel agonists and antagonists, such as DHPs, phenylalkylamines, omega conotoxins (xcfx89-CgTx), the funnel web spider toxin xcfx89-Aga-IV, pyrazonoylguanidines and or in other physical and structural properties. These subunit types also appear to differ in the holding potential and in the kinetics of currents produced upon depolarization of cell membranes containing calcium channels that include different types of xcex11 subunits.
DNA that encodes an xcex11 subunit that binds to at least one compound selected from among dihydropyridines, phenylalkylamines, xcfx89-CgTx, components of funnel web spider toxin, and pyrazonoylguanidines is provided. For example, the xcex11B subunit provided herein appears to specifically interact with xcfx89-CgTx in N-type channels, and the xcex11D subunit provided herein specifically interacts with DHPs in L-type channels.
Identification and Isolation of DNA Encoding the xcex11D Human Calcium Channel Subunit
The xcex11D subunit cDNA has been isolated using fragments of the rabbit skeletal muscle calcium channel xcex11 subunit cDNA as a probe to screen a cDNA library of a human neuroblastoma cell line, IMR32, to obtain clone xcex11.36. This clone was used as a probe to screen additional IMR32 cell cDNA libraries to obtain overlapping clones, which were then employed for screening until a sufficient series of clones to span the length of the nucleotide sequence encoding the human xcex11D subunit was obtained. Full-length clones encoding xcex11D were constructed by ligating portions of partial xcex11D clones as described in Example II. SEQ ID No. 1 shows the 7,635 nucleotide sequence of the cDNA encoding the xcex11D subunit. There is a 6,483 nucleotide sequence reading frame which encodes a sequence of 2,161 amino acids (as set forth in SEQ ID No. 1).
SEQ ID No. 2 provides the sequence of an alternative exon encoding the IS6 transmembrane domain [see Tanabe, T., et al. (1987) Nature 328:313-318 for a description of transmembrane domain terminology] of the xcex11D subunit.
SEQ ID No. 1 also shows the 2,161 amino acid sequence deduced from the human neuronal calcium channel xcex11D subunit DNA. Based on the amino acid sequence, the xcex11D protein has a calculated Mr of 245,163. The xcex11D subunit of the calcium channel contains four putative internal repeated sequence regions. Four internally repeated regions represent 24 putative transmembrane segments, and the amino- and carboxyl-termini extend intracellularly.
The xcex11D subunit has been shown to mediate DHP-sensitive, high-voltage-activated, long-lasting calcium channel activity. This calcium channel activity was detected when oxc3x6cytes were co-injected with RNA transcripts encoding an xcex11D and xcex21-2 or xcex11D, xcex12b and xcex21-2 subunits. This activity was distinguished from Ba2+ currents detected when oxc3x6cytes were injected with RNA transcripts encoding the xcex21-2xc2x1xcex12b subunits. These currents pharmacologically and biophysically resembled Ca2+ currents reported for uninjected oxc3x6cytes.
Identification and Isolation of DNA Encoding the xcex11A Human Calcium Channel Subunit
Biological material containing DNA encoding a portion of the xcex11A subunit had been deposited in the American Type Culture Collection, 12301 Parklawn Drive, Rockville, Md. 20852 U.S.A. under the terms of the Budapest Treaty on the International Recognition of Deposits of Microorganisms for Purposes of Patent Procedure and the Regulations promulgated under this Treaty. Samples of the deposited material are and will be available to industrial property offices and other persons legally entitled to receive them under the terms of the Treaty and Regulations and otherwise in compliance with the patent laws and regulations of the United States of America and all other nations or international organizations in which this application, or an application claiming priority of this application, is filed or in which any patent granted on any such application is granted.
A portion of an xcex11A subunit is encoded by an approximately 3 kb insert in xcexgt10 phage designated xcex11.254 in E. coli host strain NM514. A phage lysate of this material has been deposited as at the American Type Culture Collection under ATCC Accession No. 75293, as described above. DNA encoding xcex11A may also be identified by screening with a probe prepared from DNA that has SEQ ID No. 21:
5xe2x80x2 CTCAGTACCATCTCTGATACCAGCCCCA 3xe2x80x2.
xcex11A splice variants have been obtained. The sequences of two xcex11A splice variants, xcex11a-1, and xcex11a-2 are set forth in SEQ. ID Nos. 22 and 23. Other splice variants may be obtained by screening a human library as described above or using all or a portion of the sequences set forth in SEQ ID Nos. 22 and 23.
Identification and Isolation of DNA Encoding the xcex11B Human Calcium Channel Subunit
DNA encoding the xcex11B subunit was isolated by screening a human basal ganglia cDNA library with fragments of the rabbit skeletal muscle calcium channel xcex11 subunit-encoding cDNA. A portion of one of the positive clones was used to screen an IMR32 cell cDNA library. Clones that hybridized to the basal ganglia DNA probe were used to further screen an IMR32 cell cDNA library to identify overlapping clones that in turn were used to screen a human hippocampus cDNA library. In this way, a sufficient series of clones to span nearly the entire length of the nucleotide sequence encoding the human xcex11B subunit was obtained. Nucleic acid amplification of specific regions of the IMR32 cell xcex11B mRNA yielded additional segments of the xcex11B coding sequence.
A full-length xcex11B DNA clone was constructed by ligating portions of the partial cDNA clones as described in Example II.C. SEQ ID Nos. 7 and 8 show the nucleotide sequences of DNA clones encoding the xcex11B subunit as well as the deduced amino acid sequences. The xcex11B subunit encoded by SEQ ID No. 7 is referred to as the xcex11B-1 subunit to distinguish it from another xcex11B subunit, xcex11B-2, encoded by the nucleotide sequence shown as SEQ ID No. 8, which is derived from alternative splicing of the xcex11B subunit transcript.
Nucleic acid amplification of IMR32 cell mRNA using oligonucleotide primers designed according to nucleotide sequences within the xcex11B-1-encoding DNA has identified variants of the xcex11B transcript that appear to be splice variants because they contain divergent coding sequences.
Identification and Isolation of DNA Encoding the xcex11C Human Calcium Channel Subunit
Numerous xcex11C-specific DNA clones were isolated. Characterization of the sequence revealed the xcex11C coding sequence, the xcex11C initiation of translation sequence, and an alternatively spliced region of xcex11C. Alternatively spliced variants of the xcex11C subunit have been identified. SEQ ID No. 3 sets forth DNA encoding a substantial protion of an xcex11C subunit. The DNA sequences set forth in SEQ ID No. 4 and No. 5 encode two possible amino terminal ends of the xcex11C protein. SEQ ID No. 6 encodes an alternative exon for the IV S3 transmembrane domain. The sequences of substantial portions of two aid splice variants, designated xcex11C-1 and xcex11C-2, are set forth in SEQ ID NOs. 3 and 36, respectively.
The isolation and identification of DNA clones encoding portions of the xcex11C subunit is described in detail in Example II.
Identification and Isolation of DNA Encoding the xcex11E Human Calcium Channel Subunit
DNA encoding xcex11E human calcium channel subunits have been isolated from an oligo dT-primed human hippocampus library. The resulting clones, which are splice variants, were designated xcex11E-1 and xcex11E-3. The subunit designated xcex11E-1 has the amino acid sequence set forth in SEQ ID No. 24, and a subunit designated xcex11E-3 has the amino acid sequence set forth in SEQ ID No. 25. These splice variants differ by virtue of a 57 base pair insert between nucleotides 2405 and 2406 of SEQ. ID No. 24.
The xcex11E subunits provided herein appear to participate in the formation of calcium channels that have properties of high-voltage activated calcium channels and low-voltage activated channels. These channels are rapidly inactivating compared to other high voltage-activated calcium channels. In addition these channels exhibit pharmacological profiles that are similar to voltage-activated channels, but are also sensitive to DHPs and xcfx89-Aga-IVA, which block certain high voltage activated channels. Additional details regarding the electrophysiology and pharmacology of channels containing xcex11E subunits is provided in Example VII. F.
Identification and Isolation of DNA Encoding the xcex11F Human Calcium Channel Subunit
Calcium channels that contain xcex11F should exhibit properties that differ from known HVA channels, formed from the xcex11A-xcex11E calcium channel subunits. Such differences may include low voltage activation, voltage-dependent inactivation, relatively high sensitivity to mibefradil and relatively high resistance to snail and arachnid toxins that inhibit most HVA channels (e.g., spider venom toxins xcfx89-AgaIIIA and xcfx89-AgaIVA and the Conus snail toxin GVIA). In addition xcex11F-subunits may be identified by homology with other xcex11-subunits and additionally by presence of an extended intracellular loop in the encoded subunit (see, e.g., SEQ No. 49, nucleotides 1506-2627) located between transmembrane domains I and II. This region in xcex11F is extended compared to other calcium channel xcex11 subunits, such as xcex11A-xcex11E.
DNA encoding an xcex11F-subunit may be isolated using the DNA provided herein. In particular, probes of at least about 16 nucleotides or 30 nucleotides or other suitable length, such 14, 30, 100 etc. bases, may be used to screen selected libraries, including mammalian DNA libraries. The selected libraries are preferably prepared from mammalian tissue or cell sources known to express T-type channels. The seqeuence of the probe is preferably based on the sequence of the intracellular loop located between transmembrane domains I and II (see, e.g., SEQ ID No. 49).
The DNA encoding the xcex11F subunit was isolated by amplifying a region of genes encoding an xcex11 subunit expressed in a human thyroid carcinoma cell line (TT cells) using degenerate oligonucleotide primers. A portion of one of the positive clones was used to further screen a human thyroid carcinoma cDNA library to identify overlapping clones that span the entire length of the nucleotide sequence encoding the human xcex11F subunit. A full-length xcex11F DNA clone can be constructed by ligating portions of the partial cDNA clones as described in Example II. SEQ ID No. 49 set forth the nucleotide sequence of a clone encoding an xcex11F subunit as well as the deduced amino acid sequence.
A comparison of the nucleic acid and deduced amino acid sequences of this xcex11F calcium channel subunit with other human xcex11 subunits reveals several distinct features. First, the intracellular loop between transmembrane Domains I and II is notably long. As exemplified in SEQ ID No. 49, the intracellular loop of human xcex11F subunit is 1,122 nt in length whereas the corresponding intracellular loops in the other human xcex11 subunits described herein range from 351 to 381 nt in length. Thus, the intracellular loop of human xcex11F is nearly 250 amino acids longer than human xcex11 subunits found in HVA calcium channels. The deduced amino acid sequence of this region (aa 420 to aa 794 of SEQ ID No. 50) contains a large number of proline residues and includes a poly-HIS region of 9 contiguous histidine residues (aa 52 to aa 528 of SEQ ID No. 50) and a region where 8 of 10 residues are alanine. The large intracellular loop located between transmembrane Domains I and II resembles the large intracellular loops found in a corresponding location in sodium channel a subunits some of which may function as homomers. It has been proposed that T-type channels have an activity that is a hybrid between HVA calcium channels and sodium channel. The xcex11F subunits provided herein may also function as sodium channels. Thus, subunits with sodium channel activity are provided.
Second, the isolated human xcex11F subunit lacks amino acid residues that are generally known to be critical (e.g., see De Waard et al. (1996) FEBS Letters 380:272-276; Pragnell et al. (1994) Nature 368:67-70) for the interaction between xcex11 subunits and the xcex2 subunits. There are at least thirteen residues located in this intracellular loop between transmembrane Domains I and II that form a motif that is highly conserved among xcex11 subunits, such as xcex11A-xcex11E described herein (see, also Pragnell et al. (1994) Nature 368:67-70).
Third, the human xcex11F subunit has another notably long extracellular loop in Domain I located between IS5 and IS6. This extracellular loop ranges from 249 to 270 nucleotide residues in other human xcex11 subunits whereas the human xcex11F subunit has 426 nucleotide residues. Other distinguishing features may be ascertained by expressing the subunit in cells as described herein.
The nucleic acid encoding the xcex11F subunit can be used to screen appropriate libraries, particularly mammaliain libraries, and more particularly mammalian libraries from tissues or cells that exhibit T-type channel activity. The encoded subunit can be identified by the above-noted distinguishing properties.
Identification and Isolation of DNA Encoding xcex2 Human Calcium Channel Subunits
DNA encoding xcex21 
To isolate DNA encoding the xcex21 subunit, a human hippocampus cDNA library was screened by hybridization to a DNA fragment encoding a rabbit skeletal muscle calcium channel xcex21 subunit. A hybridizing clone was selected and was in turn used to isolate overlapping clones until the overlapping clones encompassing DNA encoding the entire human calcium channel xcex2 subunit were isolated and sequenced.
Five alternatively spliced forms of the human calcium channel xcex21 subunit have been identified and DNA encoding a number of forms have been isolated. These forms are designated xcex21-1, expressed in skeletal muscle, xcex21-2, expressed in the CNS, xcex21-3, also expressed in the in the CNS, xcex21-4, expressed in aorta tissue and HEK 293 cells, and xcex21-5, expressed in HEK 293 cells. Full-length DNA clones encoding the xcex21-2 and xcex21-3 subunits have been constructed. The subunits xcex21-1, xcex21-2, xcex21-4 and xcex21-5 have been identified by nucleic acid amplification analysis as alternatively spliced forms of the xcex2 subunit. Sequences of the xcex21 splice variants are set forth in SEQ ID Nos. 9, 10 and 33-35.
DNA encoding xcex22 
DNA encoding the xcex22 splice variants has been obtained. These splice variants include xcex22C-xcex22E. Splice variants xcex22C-xcex22E include all of sequence set forth in SEQ ID No. 26, except for the portion at the 5xe2x80x2 end (up to nucleotide 182), which differs among splice variants. The sequence set forth in SEQ ID No. 26 encodes xcex22D. Additional splice variants may be isolated using the methods described herein and oligonucleotides including all or portions of the DNA set forth in SEQ ID. No. 26 or may be prepared or obtained as described in the Examples. The sequences of xcex22 splice variants xcex22C and xcex22E are set forth in SEQ ID Nos. 37 and 38, respectively.
DNA encoding xcex23 
DNA encoding the xcex23 subunit and any splice variants thereof may be isolated by screening a library, as described above for the xcex21 subunit, using DNA probes prepared according to SEQ ID Nos. 19, 20 or using all or a portion of the deposited xcex23 clone plasmid xcex21.42 (ATCC Accession No. 69048).
The E. coli host containing plasmid xcex21.42 that includes DNA encoding a xcex23 subunit has been deposited as ATCC Accession No. 69048 in the American Type Culture Collection, 12301 Parklawn Drive, Rockville, Md. 20852 U.S.A. under the terms of the Budapest Treaty on the International Recognition of Deposits of Microorganisms for Purposes of Patent Procedure and the Regulations promulgated under this Treaty. Samples of the deposited material are and will be available to industrial property offices and other persons legally entitled to receive them under the terms of the Treaty and Regulations and otherwise in compliance with the patent laws and regulations of the United States of America and all other nations or international organizations in which this application, or an application claiming priority of this application, is filed or in which any patent granted on any such application is granted.
The xcex23 encoding plasmid is designated xcex21.42. The plasmid contains a 2.5 kb EcoRI fragment encoding xcex23 inserted into vector pGem(copyright)7zF(+) and has been deposited in E. coli host strain DH5xcex1. The sequences of xcex23 splice variants, designated xcex23-1 and xcex23-2 are set forth in SEQ ID Nos. 19 and 20, respectively.
Identification and Isolation of DNA Encoding the xcex12 Human Calcium Channel Subunit
DNA encoding a human neuronal calcium channel xcex12 subunit was isolated in a manner substantially similar to that used for isolating DNA encoding an xcex11 subunit, except that a human genomic DNA library was probed under low and high stringency conditions with a fragment of DNA encoding the rabbit skeletal muscle calcium channel xcex12 subunit. The fragment included nucleotides having a sequence corresponding to the nucleotide sequence between nucleotides 43 and 272 inclusive of rabbit back skeletal muscle calcium channel xcex12 subunit cDNA as disclosed in PCT International Patent Application Publication No. WO 89/09834, which corresponds to U.S. application Ser. No. 07/620,520 (now allowed U.S. application Ser. No. 07/914,231), which is a continuation-in-part of U.S. Ser. No. 176,899, filed Apr. 4, 1988, which applications have been incorporated herein by reference. Example IV describes the isolation of DNA clones encoding xcex12 subunits of a human calcium channel from a human DNA library using genomic DNA and cDNA clones, identified by hybridization to the genomic DNA, as probes.
SEQ ID Nos. 11 and 29-32 show the sequence of DNA encoding xcex12 subunits. As described in Example V, nucleic acid amplification analysis of RNA from human skeletal muscle, brain tissue and aorta using oligonucleotide primers specific for a region of the human neuronal xcex12 subunit cDNA that diverges from the rabbit skeletal muscle calcium channel xcex12 subunit cDNA identified splice variants of the human calcium channel xcex12 subunit transcript.
Identification and Isolation of DNA Encoding xcex3 Human Calcium Channel Subunits
DNA encoding a portion of a human neuronal calcium channel xcex3 subunit has been isolated as described in detail in Example VI. SEQ ID No. 14 shows the nucleotide sequence at the 3xe2x80x2-end of this DNA which includes a reading frame encoding a sequence of 43 amino acid residues. Since the portion that has been obtained is homologous to the rabbit clone, described in allowed co-owned U.S. application Ser. No. 07/482,384, the remainder of the clone can be obtained using routine methods.
Antibodies
Antibodies, monoclonal or polyclonal, specific for calcium channel subunit subtypes or for calcium channel types can be prepared employing standard techniques, known to those of skill in the art, using the subunit proteins or portions thereof as antigens. Anti-peptide and anti-fusion protein antibodies can be used [see, for example, Bahouth et al. (1991) Trends Pharmacol. Sci. 12:338-343; Current Protocols in Molecular Biology (Ausubel et al., eds.) John Wiley and Sons, New York (1984)]. Factors to consider in selecting portions of the calcium channel subunits for use as immunogens (as either a synthetic peptide or a recombinantly produced bacterial fusion protein) include antigenicity accessibility (i.e., extracellular and cytoplasmic domains), uniqueness to the particular subunit, and other factors known to those of skill in this art.
The availability of subunit-specific antibodies makes possible the application of the technique of immunohistochemistry to monitor the distribution and expression density of various subunits (e.g., in normal vs diseased brain tissue). Such antibodies could also be employed in diagnostic, such as LES diagnosis, and therapeutic applications, such as using antibodies that modulate activities of calcium channels.
The antibodies can be administered to a subject employing standard methods, such as, for example, by intraperitoneal, intramuscular, intravenous, or subcutaneous injection, implant or transdermal modes of administration. One of skill in the art can empirically determine dosage forms, treatment regiments, and other paremeters, depending on the mode of administration employed.
Subunit-specific monoclonal antibodies and polyclonal antisera have been prepared. The regions from which the antigens were derived were identified by comparing the DNA and amino acid sequences of all known a or xcex2 subunit subtypes. Regions of least homology, preferably human-derived sequences were selected. The selected regions or fusion proteins containing the selected regions are used as immunogens. Hydrophobicity analyses of residues in selected protein regions and fusion proteins are also performed; regions of high hydrophobicity are avoided. Also, and more importantly, when preparing fusion proteins in bacterial hosts, rare codons are avoided. In particular, inclusion of 3 or more successive rare codons in a selected host is avoided. Numerous antibodies, polyclonal and monoclonal, specific for xcex1 or xcex2 subunit types or subtypes have been prepared; some of these are listed in the following Table. Exemplary antibodies and peptide antigens used to prepare the antibodies are set forth Table 3:
The GST fusion proteins are each specific for the cytoplasmic loop region IIS6-IIS1, which is a region of low subtype homology for all subtypes, including xcex11C and xcex11D, for which similar fusions and antisera can be prepared.
Preparation of Recombinant Eukaryotic Cells Containing DNA Encoding Heterologous Calcium Channel Subunits
DNA encoding one or more of the calcium channel subunits or a portion of a calcium channel subunit may be introduced into a host cell for expression or replication of the DNA. Such DNA may be introduced using methods described in the following examples or using other procedures well known to those skilled in the art. Incorporation of cloned DNA into a suitable expression vector, transfection of eukaryotic cells with a plasmid vector or a combination of plasmid vectors, each encoding one or more distinct genes or with linear DNA, and selection of transfected cells are also well known in the art [see, e.g., Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press].
Cloned full-length nucleic acid encoding any of the subunits of a calcium channel may be introduced into a plasmid vector for expression in a eukaryotic cell. Such nucleic acid may be genomic DNA or cDNA or RNA. Presently preferred cells are those containing heterologous DNA encoding an xcex11F subunit. Host cells may be transfected with one or a combination of the plasmids, each of which encodes at least one calcium channel subunit. Alternatively, host cells may be transfected with linear DNA using methods well known to those of skill in the art.
While the DNA provided herein may be expressed in any eukaryotic cell, including yeast cells such as P. pastoris [see, e.g., Cregg et al. (1987) Bio/Technology 5:479], mammalian expression systems for expression of the DNA encoding the human calcium channel subunits provided herein are preferred.
The heterologous DNA may be introduced by any method known to those of skill in the art, such as transfection with a vector encoding the heterologous DNA. Particularly preferred vectors for transfection of mammalian cells are the pSV2dhfr expression vectors, which contain the SV40 early promoter, mouse dhfr gene, SV40 polyadenylation and splice sites and sequences necessary for maintaining the vector in bacteria, cytomegalovirus (CMV) promoter-based vectors such as pCDNA1, or pcDNA-amp and MMTV promoter-based vectors. DNA encoding the human calcium channel subunits has been inserted in the vector pCDNA1 at a position immediately following the CMV promoter. The vector pCDNA1 is presently preferred.
Stably or transiently transfected mammalian cells may be prepared by methods known in the art by transfecting cells with an expression vector having a selectable marker gene such as the gene for thymidine kinase, dihydrofolate reductase, neomycin resistance or the like, and, for transient transfection, growing the transfected cells under conditions selective for cells expressing the marker gene. Functional voltage-dependent calcium channels have been produced in HEK 293 cells transfected with a derivative of the vector pCDNA1 that contains DNA encoding a human calcium channel subunit.
The heterologous DNA may be maintained in the cell as an episomal element or may be integrated into chromosomal DNA of the cell. The resulting recombinant cells may then be cultured or subcultured (or passaged, in the case of mammalian cells) from such a culture or a subculture thereof. Methods for transfection, injection and culturing recombinant cells are known to the skilled artisan. Eukaryotic cells in which DNA or RNA may be introduced, include any cells that are transfectable by such DNA or RNA or into which such DNA may be injected. Virtually any eukaryotic cell can serve as a vehicle for heterologous DNA. Preferred cells are those that can also express the DNA and RNA and most preferred cells are those that can form recombinant or heterologous calcium channels that include one or more subunits encoded by the heterologous DNA. Such cells may be identified empirically or selected from among those known to be readily transfected or injected. Preferred cells for introducing DNA include those that can be transiently or stably transfected and include, but are not limited to, cells of mammalian origin, such as COS cells, mouse L cells, CHO cells, human embryonic kidney cells, African green monkey cells and other such cells known to those of skill in the art, amphibian cells, such as Xenopus laevis oxc3x6cytes, or those of yeast such as Saccharomyces cerevisiae or Pichia pastoris. Preferred cells for expressing injected RNA transcripts or cDNA include Xenopus laevis oxc3x6bcytes. Cells that are preferred for transfection of DNA are those that can be readily and efficiently transfected. Such cells are known to those of skill in the art or may be empirically identified. Preferred cells include DG44 cells and HEK 293 cells, particularly HEK 293 cells that can be frozen in liquid nitrogen and then thawed and regrown. Such HEK 293 cells are described, for example in U.S. Pat. No. 5,024,939 to Gorman [see, also Stillman et al. (1985) Mol. Cell. Biol. 5:2051-2060].
The cells may be used as vehicles for replicating heterologous DNA introduced therein or for expressing the heterologous DNA introduced therein. In certain embodiments, the cells are used as vehicles for expressing the heterologous DNA as a means to produce substantially pure human calcium channel subunits or heterologous calcium channels. Host cells containing the heterologous DNA may be cultured under conditions whereby the calcium channels are expressed. The calcium channel subunits may be purified using protein purification methods known to those of skill in the art. For example, antibodies, such as those provided herein, that specifically bind to one or more of the subunits may be used for affinity purification of the subunit or calcium channels containing the subunits.
Substantially pure subunits of a human calcium channel xcex11 subunits of a human calcium channel, xcex12 subunits of a human calcium channel, xcex2 subunits of a human calcium channel and xcex3 subunits of a human calcium channel are provided. Substantially pure isolated calcium channels that contain at least one of the human calcium channel subunits are also provided. Substantially pure calcium channels that contain a mixture of one or more subunits encoded by the host cell and one or more subunits encoded by heterologous DNA or RNA that has been introduced into the cell are also provided. Substantially pure subtype- or tissue-type specific calcium channels are also provided.
In one embodiment, eukaryotic cells that contain heterologous DNA encoding at least one of xcex11 subunit of a calcium channel, preferably an xcex11F subunit, that express the xcex11F subunit and form functional homomeric human xcex11F-containing calcium channels are provided. These cells may be used to screen for compounds that modulate the activity of T-type channels and LVA type calcium channels.
In other embodiments, eukaryotic cells that contain heterologous DNA encoding at least one of an xcex11 subunit of a human calcium channel, an xcex12 subunit of a human calcium channel, a xcex2 subunit of a human calcium channel and a xcex3 subunit of a human calcium channel are provided. In accordance with one preferred embodiment, the heterologous DNA is expressed in the eukaryotic cell and preferably encodes a human calcium channel xcex11 subunit.
Expression of Heterologous Calcium Channels: Electrophysiology and Pharmacology
Electrophysiological methods for measuring calcium channel activity are known to those of skill in the art and are exemplified herein. Any such methods may be used in order to detect the formation of functional calcium channels and to characterize the kinetics and other characteristics of the resulting currents. Pharmacological studies may be combined with the electrophysiological measurements in order to further characterize the calcium channels.
With respect to measurement of the activity of functional heterologous calcium channels, preferably, endogenous ion channel activity and, if desired, heterologous channel activity of channels that do not contain the desired subunits, of a host cell can be inhibited to a significant extent by chemical, pharmacological and electrophysiological means, including the use of differential holding potential, to increase the S/N ratio of the measured heterologous calcium channel activity.
Thus, various combinations of subunits encoded by the DNA provided herein are introduced into eukaryotic cells. The resulting cells can be examined to ascertain whether functional channels are expressed and to determine the properties of the channels. In particularly preferred aspects, the eukaryotic cell which contains the heterologous DNA expresses it and forms a recombinant functional calcium channel activity. In more preferred aspects, the recombinant calcium channel activity is readily detectable because it is a type that is absent from the untransfected host cell or is of a magnitude and/or pharmacological properties or exhibits biophysical properties not exhibited in the untransfected cell.
The eukaryotic cells can be transfected with various combinations of the subunit subtypes provided herein. The resulting cells will provide a uniform population of calcium channels for study of calcium channel activity and for use in the drug screening assays provided herein. Experiments that have been performed have demonstrated the inadequacy of prior classification schemes.
Preferred among transfected cells is a recombinant eukaryotic cell with a functional heterologous calcium channel. The recombinant cell can be produced by introduction of and expression of heterologous DNA or RNA transcripts encoding an xcex11 subunit of a human calcium channel as a homomer, more preferably also expressing, a heterologous DNA encoding a xcex2 subunit of a human calcium channel and/or heterologous DNA encoding an xcex12 subunit of a human calcium channel. Especially preferred is the expression in such a recombinant cell of each of the xcex11, xcex2 and xcex12 subunits encoded by such heterologous DNA or RNA transcripts, and optionally expression of heterologous DNA or an RNA transcript encoding a xcex3 subunit of a human calcium channel. The functional calcium channels may preferably include at least an xcex11 subunit and a xcex2 subunit of a human calcium channel. Eukaryotic cells expressing these two subunits and also cells expressing additional subunits, have been prepared by transfection of DNA and by injection of RNA transcripts. Such cells have exhibited voltage-dependent calcium channel activity attributable to calcium channels that contain one or more of the heterologous human calcium channel subunits. For example, eukaryotic cells expressing heterologous calcium channels containing an xcex12 subunit in addition to the xcex11 subunit and a xcex2 subunit have been shown to exhibit increased calcium selective ion flow across the cellular membrane in response to depolarization, indicating that the xcex12 subunit may potentiate calcium channel function. Cells that have been co-transfected with increasing ratios of xcex12 to xcex11 and the activity of the resulting calcium channels has been measured. The results indicate that increasing the amount of xcex12-encoding DNA relative to the other transfected subunits increases calcium channel activity.
Eukaryotic cells that express heterologous calcium channels containing a human xcex11 subunit as a homomer, particularly the xcex11F subunit, or at least a human xcex11 subunit and optionally an xcex12xcex4 subunit and/or a human xcex2 subunit are preferred. Eukaryotic cells transformed with a composition containing DNA or an RNA transcript that encodes an xcex11 subunit alone or in combination with a xcex2 and/or an xcex12 subunit may be used to produce cells that express functional calcium channels. Since recombinant cells expressing human calcium channels containing all of the human subunits encoded by the heterologous DNA or RNA are especially preferred, it is desirable to inject or transfect such host cells with a sufficient concentration of the subunit encoding nucleic acids to form calcium channels that contain the human subunits encoded by heterologous DNA or RNA. The precise amounts and ratios of DNA or RNA encoding the subunits may be empirically determined and optimized for a particular combination of subunits, cells and assay conditions.
In particular, mammalian cells have been transiently and stably transfected with DNA encoding one or more human calcium channel subunits. Such cells express heterologous calcium channels that exhibit pharmacological and electrophysiological properties that can be ascribed to human calcium channels. Such cells, however, represent homogeneous populations and the pharmacological and electrophysiological data provides insights into human calcium channel activity heretofore unattainable. For example, HEK cells that have been transiently transfected with DNA encoding the xcex11E-1, xcex12b, and xcex21-3 subunits. The resulting cells transiently express these subunits, which form calcium channels that have properties that appear to be a pharmacologically distinct class of voltage-activated calcium channels distinct from those of L-, N-, T- and P-type channels. The observed xcex11E currents were insensitive to drugs and toxins previously used to define other classes of voltage-activated calcium channels.
HEK cells that have been transiently transfected with DNA encoding xcex11B-1, xcex12b, and xcex21-2 express heterologous calcium channels that exhibit sensitivity to xcfx89-conotoxin and currents typical of N-type channels. It has been found that alteration of the molar ratios of xcex11B-1, xcex12b and xcex21-2 introduced into the cells to achieve equivalent mRNA levels significantly increased the number of receptors per cell, the current density, and affected the Kd for xcfx89-conotoxin.
The electrophysiological properties of these channels produced from xcex11B-1, xcex12b, and xcex21-2 was compared with those of channels produced by transiently transfecting HEK cells with DNA encoding xcex11B-1, xcex12b and xcex21-3. The channels exhibited similar voltage dependence of activation, substantially identical voltage dependence, similar kinetics of activation and tail currents that could be fit by a single exponential. The voltage dependence of the kinetics of inactivation was significantly different at all voltages examined.
In certain embodiments, the eukaryotic cell with a heterologous calcium channel is produced by introducing into the cell a first composition, which contains at least one RNA transcript that is translated in the cell into a subunit of a human calcium channel. In preferred embodiments, the subunits that are translated include an xcex11 subunit of a human calcium channel. More preferably, the composition that is introduced contains an RNA transcript which encodes an xcex11 subunit of a human calcium channel and also contains (1) an RNA transcript which encodes a xcex2 subunit of a human calcium channel and/or (2) an RNA transcript which encodes an xcex12 subunit of a human calcium channel. Especially preferred is the introduction of RNA encoding an xcex11, a xcex2 and an xcex12 human calcium channel subunit, and, optionally, a xcex3 subunit of a human calcium channel. Methods for in vitro transcription of a cloned DNA and injection of the resulting RNA into eukaryotic cells are well known in the art. Transcripts of any of the full-length DNA encoding any of the subunits of a human calcium channel may be injected alone or in combination with other transcripts into eukaryotic cells for expression in the cells. Amphibian oocytes are particularly preferred for expression of in vitro transcripts of the human calcium channel subunit cDNA clones provided herein. Amphibian oocytes that express functional heterologous calcium channels have been produced by this method.
Assays and Clinical uses of the Cells and Calcium Channels
Assays
Assays for Identifying Compounds that Modulate Calcium Channel Activity
Among the uses for eukaryotic cells which recombinantly express one or more subunits are assays for determining whether a test compound has calcium channel agonist or antagonist activity. These eukaryotic cells may also be used to select from among known calcium channel agonists and antagonists those exhibiting a particular calcium channel subtype specificity and to thereby select compounds that have potential as disease- or tissue-specific therapeutic agents.
In vitro methods for identifying compounds, such as calcium channel agonist and antagonists, that modulate the activity of calcium channels using eukaryotic cells that express heterologous human calcium channels are provided.
In particular, the assays use eukaryotic cells that express homomeric or heteromeric human calcium channel subunits encoded by heterologous DNA provided herein, for screening potential calcium channel agonists and antagonists which are specific for human calcium channels and particularly for screening for compounds that are specific for particular human calcium channel subtypes. Such assays may be used in conjunction with methods of rational drug design to select among agonists and antagonists, which differ slightly in structure, those particularly useful for modulating the activity of human calcium channels, and to design or select compounds that exhibit subtype- or tissue-specific calcium channel antagonist and agonist activities. These assays should accurately predict the relative therapeutic efficacy of a compound for the treatment of certain disorders in humans. In addition, since subtype-and tissue-specific calcium channel subunits are provided, cells with tissue-specific or subtype-specific recombinant calcium channels may be prepared and used in assays for identification of human calcium channel tissue- or subtype-specific drugs.
Desirably, the host cell for the expression of calcium channel subunits does not produce endogenous calcium channel subunits of the type or in an amount that substantially interferes with the detection of heterologous calcium channel subunits in ligand binding assays or detection of heterologous calcium channel function, such as generation of calcium current, in functional assays. Also, the host cells preferably should not produce endogenous calcium channels which detectably interact with compounds having, at physiological concentrations (generally nanomolar or picomolar concentrations), affinity for calcium channels that contain one or all of the human calcium channel subunits provided herein.
With respect to ligand binding assays for identifying a compound which has affinity for calcium channels, cells are employed which express, preferably, at least a heterologous xcex11 subunit. Transfected eukaryotic cells which express at least an xcex11 subunit may be used to determine the ability of a test compound to specifically bind to heterologous calcium channels by, for example, evaluating the ability of the test compound to inhibit the interaction of a labeled compound known to specifically interact with calcium channels. Such ligand binding assays may be performed on intact transfected cells or membranes prepared therefrom.
The capacity of a test compound to bind to or otherwise interact with membranes that contain heterologous calcium channels or subunits thereof, preferably xcex11F subunit-containing calcium channels, may be determined by using any appropriate method, such as competitive binding analysis, such as Scatchard plots, in which the binding capacity of such membranes is determined in the presence and absence of one or more concentrations of a compound having known affinity for the calcium channel. Where necessary, the results may be compared to a control experiment designed in accordance with methods known to those of skill in the art. For example, as a negative control, the results may be compared to those of assays of an identically treated membrane preparation from host cells which have not been transfected with one or more subunit-encoding nucleic acids.
The assays involve contacting the cell membrane of a recombinant eukaryotic cell which expresses at least one subunit of a human calcium channel, preferably at least an xcex11 subunit of a human calcium channel, with a test compound and measuring the ability of the test compound to specifically bind to the membrane or alter or modulate the activity of a heterologous calcium channel on the membrane.
In preferred embodiments, the assay uses a recombinant cell that has a calcium channel containing an xcex11 subunit of a human calcium channel. In other preferred embodiments, the assay uses a recombinant cell that has a calcium channel containing an xcex11 subunit of a human calcium channel in combination with a xcex2 subunit of a human calcium channel and/or an xcex12 subunit of a human calcium channel. Recombinant cells expressing heterologous calcium channels containing each of the xcex11 and optionally a xcex2 and/or xcex12 human subunits, and, optionally, a xcex3 subunit of a human calcium channel are especially preferred for use in such assays.
In certain embodiments, the assays for identifying compounds that modulate calcium channel activity are practiced by measuring the calcium channel activity of a eukaryotic cell having a heterologous, functional calcium channel when such cell is exposed to a solution containing the test compound and a calcium channel-selective ion and comparing the measured calcium channel activity to the calcium channel activity of the same cell or a substantially identical control cell in a solution not containing the test compound. The cell is maintained in a solution having a concentration of calcium channel-selective ions sufficient to provide an inward current when the channels open. Recombinant cells expressing calcium channels that include each of the xcex11, xcex2 and xcex12 human subunits, and, optionally, a xcex3 subunit of a human calcium channel, are especially preferred for use in such assays. Methods for practicing such assays are known to those of skill in the art. For example, for similar methods applied with Xenopus laevis oxc3x6cytes and acetylcholine receptors, see, Mishina et al. [(1985) Nature 313:364] and, with such oxc3x6cytes and sodium channels [see, Noda et al. (1986) Nature 322:826-828]. For similar studies which have been carried out with the acetylcholine receptor, see, e.g., Claudio et al. [(1987) Science 238:1688-1694]. Transcription based assays are also contemplated herein.
Functional recombinant or heterologous calcium channels may be identified by any method known to those of skill in the art. For example, electrophysiological procedures for measuring the current across an ion-selective membrane of a cell, which are well known, may be used. The amount and duration of the flow of calcium-selective ions through heterologous calcium channels of a recombinant cell containing DNA encoding one or more of the subunits provided herein has been measured using electrophysiological recordings using a two electrode and the whole-cell patch clamp techniques. In order to improve the sensitivity of the assays, known methods can be used to eliminate or reduce non-calcium currents and calcium currents resulting from endogenous calcium channels, when measuring calcium currents through recombinant channels. For example, the DHP Bay K 8644 specifically enhances L-type calcium channel function by increasing the duration of the open state of the channels [see, e.g., Hess, J. B., et al. (1984) Nature 311:538-544]. Prolonged opening of the channels results in calcium currents of increased magnitude and duration. Tail currents can be observed upon repolarization of the cell membrane after activation of ion channels by a depolarizing voltage command. The opened channels require a finite time to close or xe2x80x9cdeactivatexe2x80x9d upon repolarization, and the current that flows through the channels during this period is referred to as a tail current. Because Bay K 8644 prolongs opening events in calcium channels, it tends to prolong these tail currents and make them more pronounced.
In practicing these assays, stably or transiently transfected cells or injected cells that express voltage-dependent human calcium channels containing one or more of the subunits of a human calcium channel desirably may be used in assays to identify agents, such as calcium channel agonists and antagonists, that modulate calcium channel activity. Functionally testing the activity of test compounds, including compounds having unknown activity, for calcium channel agonist or antagonist activity to determine if the test compound potentiates, inhibits or otherwise alters the flow of calcium ions or other ions through a human calcium channel can be accomplished by (a) maintaining a eukaryotic cell which is transfected or injected to express a heterologous functional calcium channel capable of regulating the flow of calcium channel-selective ions into the cell in a medium containing calcium channel-selective ions (i) in the presence of and (ii) in the absence of a test compound; (b) maintaining the cell under conditions such that the heterologous calcium channels are substantially closed and endogenous calcium channels of the cell are substantially inhibited (c) depolarizing the membrane of the cell maintained in step (b) to an extent and for an amount of time sufficient to cause (preferably, substantially only) the heterologous calcium channels to become permeable to the calcium channel-selective ions; and (d) comparing the amount and duration of current flow into the cell in the presence of the test compound to that of the current flow into the cell, or a substantially similar cell, in the absence of the test compound.
The assays thus use cells, provided herein, that express heterologous functional calcium channels and measure functionally, such as electrophysiologically, the ability of a test compound to potentiate, antagonize or otherwise modulate the magnitude and duration of the flow of calcium channel-selective ions, such as Ca2+ or Ba2+, through the heterologous functional channel. The amount of current which flows through the recombinant calcium channels of a cell may be determined directly, such as electrophysiologically, or by monitoring an independent reaction which occurs intracellularly and which is directly influenced in a calcium (or other) ion dependent manner. Any method for assessing the activity of a calcium channel may be used in conjunction with the cells and assays provided herein. For example, in one embodiment of the method for testing a compound for its ability to modulate calcium channel activity, the amount of current is measured by its modulation of a reaction which is sensitive to calcium channel-selective ions and uses a eukaryotic cell which expresses a heterologous calcium channel and also contains a transcriptional control element operatively linked for expression to a structural gene that encodes an indicator protein. The transcriptional control element used for transcription of the indicator gene is responsive in the cell to a calcium channel-selective ion, such as Ca2+ and Ba2+. The details of such transcriptional based assays are described in commonly owned PCT International Patent Application No. PCT/US91/5625, filed Aug. 7, 1991, which claims priority to copending commonly owned allowed U.S. application Ser. No. 07/563,751, filed Aug. 7, 1990; see also, commonly owned published PCT International Patent Application PCT US92/11090, which corresponds to co-pending U.S. applications Ser. Nos. 08/229,150 and 08/244,985. The contents of these applications are herein incorporated by reference thereto.
Assays for Diagnosis of LES
LES is an autoimmune disease characterized by an insufficient release of acetylcholine from motor nerve terminals which normally are responsive to nerve impulses. Immunoglobulins (IgG) from LES patients block individual voltage-dependent calcium channels and thus inhibit calcium channel activity [Kim and Neher, Science 239:405-408 (1988)]. A diagnostic assay for Lambert Eaton Syndrome (LES) is provided herein. The diagnostic assay for LES relies on the immunological reactivity of LES IgG with the human calcium channels or particular subunits alone or in combination or expressed on the surface of recombinant cells. For example, such an assay may be based on immunoprecipitation of LES IgG by the human calcium channel subunits and cells that express such subunits provided herein.
Clinical applications
In relation to therapeutic treatment of various disease states, the availability of DNA encoding human calcium channel subunits permits identification of any alterations in such genes (e.g., mutations) which may correlate with the occurrence of certain disease states. In addition, the creation of animal models of such disease states becomes possible, by specifically introducing such mutations into synthetic DNA fragments that can then be introduced into laboratory animals or in vitro assay systems to determine the effects thereof.
Also, genetic screening can be carried out using the nucleotide sequences as probes. Thus, nucleic acid samples from subjects having pathological conditions suspected of involving alteration/modification of any one or more of the calcium channel subunits can be screened with appropriate probes to determine if any abnormalities exist with respect to any of the endogenous calcium channels. Similarly, subjects having a family history of disease states related to calcium channel dysfunction can be screened to determine if they are also predisposed to such disease states.